Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Dnmt3a

Cell type

Cell type Class
Neural
Cell type
Cerebral Cortex
MeSH Description
Type of cerebral cortex which does not pass through a perinatal phase of six-layered structure as in the NEOCORTEX and develops into three or four layers in the mature brain. Allocortex has three subareas: archi- paleo- and periallo-cortex.

Attributes by original data submitter

Sample

source_name
Cerebral cortex
tissue
Cerebral cortex
strain
C57BL/6
genotype
Dnmt3a1_delta_N
developmental stage
postnatal day 21
chip antibody
anti-DNMT3A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cerebral cortex was isolated, crushed and homogenized briefly by pipetting. Tissues were cross-linked in 1% formaldehyde and sheared with a Covaris M220 Ultrasonicator. ChIP-Seq Libraries were prepared with ThruPLEX® DNA-seq 48D Kit (Rubicon Genomics).

Sequencing Platform

instrument_model
NextSeq 2000

mm10

Number of total reads
53789194
Reads aligned (%)
82.1
Duplicates removed (%)
59.3
Number of peaks
204 (qval < 1E-05)

mm9

Number of total reads
53789194
Reads aligned (%)
82.0
Duplicates removed (%)
59.3
Number of peaks
180 (qval < 1E-05)

Base call quality data from DBCLS SRA